3GDJ

Crystal structure determination of camel(Camelus dromedarius)hemoglobin at 2 angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PGH	PDB ENTRY 2PGH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	293	0.003ml of protein solution with 0.002ml of 45% PEG 3350 in 50mM of phosphate buffer at pH 6.8 with 1 M NaCl equilibrated against 1 ml of reservoir containing the same solution, VAPOR DIFFUSION, HANGING DROP, temperature 293KK

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.759	α = 90
b = 116.782	β = 120.07
c = 52.807	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2009-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5417

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	20	94.2	0.0774	5.2	2.43	87740	35552	2.3	2.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	92.4		0.3202	1	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2PGH	2	20	31890	31638	3491	94.22	0.23062	0.22358	0.29471	RANDOM	31.02

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
1.18		-0.19	-2.92		1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.391
r_dihedral_angle_3_deg	16.245
r_dihedral_angle_4_deg	14.883
r_dihedral_angle_1_deg	5.127
r_scangle_it	1.712
r_angle_refined_deg	1.118
r_scbond_it	1.118
r_mcangle_it	0.761
r_mcbond_it	0.435
r_nbtor_refined	0.287
r_symmetry_vdw_refined	0.217
r_nbd_refined	0.189
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.149
r_metal_ion_refined	0.146
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4428
Nucleic Acid Atoms
Solvent Atoms	339
Heterogen Atoms	172

Software

Software
Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling